Allright,
I just committed support for markdown descriptions. It is still in master, and haven't cut a new gem yet, but you can certainly give it a try.
Any description for controllers, actions, attributes, mediatypes...etc would be rendered as markdown.
Remember that, this means that HTML would render perfectly fine too.
Also, know that, if the description text starts indented with 4 spaces or more, it'll be interpreted as a code block (and therefore rendered with a surrounding code box etc). I'm just saying this since I happen to try it with an example app that had a description defined through a heredoc, which was all indented many spaces, and it took me a moment to figure that out.
@alistair linking can happen as normal markdown/html tags, obviously. What we need to formalize a little more is the routing on the doc browser, so you can easily create the hrefs to resources or types. The good news there is that the "ids" for the routes of controllers and types are consistent now, and should be very easy to construct by using their "id" method (and knowing the appropriate prefix).
Cheers,
Josep M.